A living plant or animal is defined according to the cellular biological activity or processes of being an organism, a thing having parts or organs. Carbon compounds are the constituent structural building blocks of the organisms of life; the chemistry of carbon is the organic chemistry of life. Autotrophic plants take in carbon as carbon dioxide and convert it to usable compounds through photosynthesis that the heterotrophic animals and fungi consume for the energy of oxidation, returning the carbon dioxide to the plants through respiration. The cycle of life. Carbon is the element of life. But the carbon cycle is more than that, it is the cycle of the earth considered as a single entity, the planet and its surrounding atmospheric environment. It is the carbon cycle that is at the core of the climate problem, as the delicate balance of atmospheric, terrestrial and pelagic carbon is offset by anthropogenic activity. Carbon dioxide is at the core of the debate about the observable increase in average temperature over the last century. According to the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) issued in 2007: "The present atmospheric CO2 concentration (367 ppm in 1999) has not been exceeded during the past 420,000 years, and likely not during the last 20 million years. The rate of increase over the past century is unprecedented, at least during the last 20,000 years. The present atmospheric CO2 increase is caused by anthropogenic emissions of CO2. About three quarters of these emissions are due to fossil fuel burning." Understanding the complexities of the carbon cycle informs the debate surrounding the nature and extent of the climate problem and the most effective actions that might be taken to address it.

Carbon and Carbon Molecular Bonding
Carbon is the 15th most common element in the earth's crust and the 4th most common in the universe (though there is the lack of accountability for dark matter to consider). Carbon is the epitome of chemical bonding among the elements due to its structure. It forms more compounds than any other element of which some ten million having been described to date. Many of the carboniferous compounds are involved in controlling the photosynthesis of plants that allow for the energy of the sun to be sequestered and involved in the respiration of animals that mobilize life. Carbon comprises about one fifth of the mass of the human body. To understand the carbon of photosynthesis, respiration and the human body, it is important first to comprehend the nature of the chemical bonding of carbon. The formation of compounds of elements in simple integer ratios (such as H2O for water) was first noted by the English schoolteacher-cum-chemist John Dalton and became the law of multiple proportions in 1805. A theory to explain this behavior of elements in compounds occurred in parallel with the discovery of the nucleus and protons by Ernest Rutherford, electrons by J. J. Thompson, and neutrons by James Chadwick in the late 19th and early 20th centuries. In 1900, Max Planck proposed quantum theory, which in simplified terms is that atomic energy levels have discreet levels called quanta and that these energy levels are proportional to the frequency of radiation, or E = h x frequency (h is Planck's constant of 6.626 x 10 -34 Joule - second). In 1913, Niels Bohr extended the notion of quantum energy levels to the electrons in an atom, postulating that electrons could only exist at certain quantum levels of energy and that each level was defined by Planck's constant. In an interesting related sidelight, in 1905 Albert Einstein applied Planck's energy to the previously observed but unexplained photoelectric effect, attributing it to the absorption of a "photon" of light by an electron that raised it to a higher energy state; the reradiation of the light was the photoelectric effect as the electron returned to its original energy level. It was for this theory (and not relativity) that Einstein first won the Nobel Prize in physics in 1921.

The quantum energy levels of the electrons around the nucleus of the atom are assigned the principal quantum numbers 1,2,3, …. or, alternatively K, L, M … the latter an artifact of spectroscopy terminology. In each principal quantum level, there are intermediate sublevels that determine the geometric shape of the electron's possible locations. These are called subshells as they represent different energy levels within the principal quantum level. They are also assigned what would seem to be random letters that also presumably derive from spectroscopy. The 's' subshell has 2 electrons, the 'p' subshell has 6 electrons, the 'd' subshell has 10 electrons and the 'f' subshell has 14 electrons. A fundamental property of science is that the components of any system will gravitate to a condition of greater stability, which is generally at the lowest energy level. In thermodynamics, the second law states that free energy in a closed system will be given up to contribute to the necessary rise in the entropy (frequently characterized as randomness). In chemistry this propensity is manifest in the chemical bond, as the electrons in the outer or valence subshell seek to establish a stable state. The first indication of stasis as the key to understanding chemical bonds was provided by those elements that don't combine with anything else, the noble or inert gases (helium, neon, argon, krypton, xenon and radon). In 1923, the American chemist Gilbert Lewis proffered the eponymous Lewis theory that has four fundamental tenets: (1) elements enter into compounds so as to share or exchange electrons; (2) in some cases the electrons are transferred from one atom to another (an ionic bond); (3) in some cases the electrons are shared between the two atoms (a covalent bond); and (4) each of the constituent atoms ends up with an "inert gas" outermost, or valence, electron shell.

Carbon in its most common isotopic form of C12 (C13 and the radioactive C14 are other forms with 1 and 2 extra neutrons respectively) has 6 protons, 6 neutrons and 6 electrons. This means that it has 2 electrons in the 1s subshell, 2 electrons in the 2s subshell and 2 electrons in the 2p subshell. The inert gas atom that carbon would seek to emulate as a matter of stability is neon, which has 10 electrons; it also has filled 1s and 2s subshells with 2 electrons, but it has also filled the 2p subshell with 6 electrons, which is apparently what makes it inert as it has no (energy) need to change. In order to achieve a total of 6 valence (outermost subshell) electrons, each carbon atom therefore needs to add 4 electrons. Hydrogen has one electron and it readily combines with carbon to form many compounds which are known collectively and logically as hydrocarbons. In the simplest configuration, one carbon shares an electron with each of 4 hydrogen atoms yielding the familiar CH4 which is methane. Carbon can also link to other carbon atoms in addition to the hydrogen atoms as exemplified by CH3 - CH3 (usually written C2H6) which is ethane; when these bonds are extended in a concatenated chain, the repeating molecular segment called mers join end-to-end to become poly-mers, or more simply polymers. However, what really makes carbon so versatile is that it can transform its outer shell structure (called hybridization) so that it can form double and triple bonds to achieve the stable neon valence configuration. At the subshell level, this means that in addition to the basic 1s22s22p2 configuration, it can also have1s22sp3 or 1s22sp2 + p or 1s22sp + p2 configurations. For example, hydrogen cyanide (HCN) is a stabile organic molecule. Nitrogen has 7 electrons and therefore needs 3 to complete the stabile neon configuration. The triple bond of carbon with nitrogen means that each atom shares the 3 electrons, so that nitrogen is stabile and carbon has the added hydrogen electron. The power of the carbon bonding regime is best exemplified by diamond, nature's hardest material. It is made up of carbon atoms each bonded to four other carbon atoms.

From the anthropogenic standpoint, the carbon cycle begins with photosynthesis. Photosynthesis is basically the production of carbohydrates and other organic molecules by the chlorophyll in green plants when provided with the appropriate environment that includes adequate light and carbon dioxide. It sounds quite simple. In reality, it is extraordinarily complicated. The circuitous conversion of the radiant energy of the sun into usable and storable chemical energy is nothing short of miraculous , even as it is the sine qua non of life. Unlocking the mystery of photosynthesis has taken decades of diligence and perspicacity on the part of chemists and biologists in combining their knowledge in the nascent discipline of biochemistry. Fundamental to the understanding of the nature of photosynthesis was the surprising discovery that oxygen, the output or product of the photosynthetic process was not from the carbon dioxide reactant but rather from the oxygen in the water molecule (H2O). The creation of a mechanism to split water into its constituents of hydrogen and oxygen with the release of the energy of its electrons to drive downstream chemical processes is the first step in a very long process to extract a carbon atom from a molecule of carbon dioxide.

The history of life on earth probably began with the ancestors of the humble blue-green alga which is now more appropriately known as a cyanobacterium since it is a prokaryotic (having no cell nucleus) bacterium and not a eukaryotic (having a cell nucleus) algal plant. It is not known exactly how or when this occurred, but it is well established that the earth's atmosphere underwent a major metamorphosis about 2.4 billion years ago in what is commonly called the "Great Oxidation Event." Oxygen went from fractions of a percent to roughly twenty percent of the atmosphere, its current level. The fossil record of cyanobacteria, though tenuous, indicates that they preceded the profound atmospheric change by some 300 million years. The prevailing hypothesis is that when oxygen first appeared the highly reduced or electron rich methane atmosphere used up the oxygen as a repository for electrons, the oxygen forming stabile oxides such as Fe2O3. In more prosaic terms, the earth had to oxidize or 'rust' first. The cyanobacteria are purportedly the progenitors for the specialized organelles called chloroplasts in plant cells in which photosynthesis takes place. This is a logical presumption in that cyanobacteria were certainly ingested and consumed by other forms of early life just as they are now. About one billion years ago, it is postulated that a cell evolved that did not consume the oxygen producing bacterium but rather retained it as a inclusion, an internal engine to absorb light and make oxygen. This Prometheus cell was the first plant, perhaps a green alga.

The complex photosynthesis process of plants involves two separate processes which are known as photosystem 2 and photosystem 1 in intentional reverse order as the order of discovery is opposite to their operative functionality. Starting in photosystem 2, two types of chlorophyll designated 'a' and 'b' with slightly different characteristics absorb incident light energy of the appropriate wavelength, mostly in the red and blue spectra. Plants appear green because chlorophyll does not absorb green which is accordingly reflected back to the observer. The absorbed photon energy is used to remove the electrons from water molecules, producing oxygen as a product - just as the cyanobacteria do. The released electrons are sent to a protein complex called a cytochrome which transports them to photosystem 1. In photosystem 1, a second infusion of photon light energy is absorbed by the chlorophyll to provide a high enough energy for the formation of the chemical known as NADPH (for Nicotinamide Adenine Dinucleotide Phosphate - an acronym is obviously necessary for rational brevity) which provides the energy input to the carbon fixation process. The full process involves more than 100 different types of proteins and more than 50,000 atoms. The process is sometimes referred to as the "Z" scheme as the graphical depiction of two energy rises with the intervening stasis look like the letter Z. Although most of the architecture of plant photosynthesis is now known, the details are still being worked out. It should be noted that so far, all that has been accomplished is to collect enough energy from the photons of sunlight in a concentrated form to use in the act of carbon fixation, that is removing one carbon atom from carbon dioxide for use in metabolism. Oxygen necessary for the electrochemical balance of the carbon cycle is released as a by-product.

The Calvin-Benson Cycle
The Bio Organic Chemistry Group was assembled at the University of California in Berkley in 1946 to take advantage of the radioactive tracer Carbon 14 in the analysis of carbon fixation with Melvin Calvin as its appointed leader. After five years of painstaking analysis by the key researchers Andrew Benson and Al Bassham, they announced their findings in the 1954 paper "The path of carbon in photosynthesis, part XXI." In what is known as the Calvin-Benson Cycle, a 5-carbon sugar called ribulose diphosphate combines with carbon dioxide to produce an unstable 6-carbon sugar that decomposes into two 3-carbon sugars that are converted by other cell proteins to glucose (C6H12O6), which is the basic sugar of energy storage in plants. The process is catalyzed by a protein called rubisco (short for ribulose biphosphate carboxylase) which has the distinction of being the most common protein on earth. The cycle actually operates such that only one of every three of the created 6-carbon sugars are extracted for metabolic purposes. The other two stay in the cycle, and, using the energy supplied by the NADPH from photosynthesis, are converted into new 5-carbon ribulose diphosphate receptors for additional carbon dioxide fixation. So that is what it takes to make sugar from the carbon dioxide of the air. Photosynthesis transfers the energy from two photons in the "Z scheme" process to NADPH which feeds into the Calvin-Benson cycle where 5-carbon molecules and carbon dioxide are catalyzed by rubisco to make the glucose precursor. All that just to get one atom of carbon from one molecule of carbon dioxide to one molecule of glucose.

Respiration, Photorespiration and C4 Plants
In what is probably one of the least understood fundamentals of botany, not only do plants convert carbon dioxide and water to glucose and oxygen through the processes of photosynthesis and the Calvin-Benson Cycle, but they also oxidize glucose to produce energy and give off carbon dioxide as a product. Respiration is defined as the oxidation of food to produce energy which in simplified chemical equation form is:

C6H12O6 + 6O2 à 6CO2 + 6H2O + energy (ATP)

All living entities including plants need energy to do things like grow new cells, repair damaged cells, and regulate the many chemical processes that are needed to maintain physiological function. Therefore, plants respire to create energy and photosynthesize to store energy. The energy is produced in the mitochondria, organelles in the cell cytoplasm that contain the enzymes to convert ATP (adenosine triphosphate) to ADP (adenosine diphosphate) and usable energy. Since photosynthesis and respiration are in many ways opposites, the oxygen created by photosynthesis can be used for respiration and the carbon dioxide created by the respiration process can be used in photosynthesis. And this is exactly what happens. When the sun is out and the leaves of the plant are illuminated, the photosynthetic process proceeds at a rate that is five to ten times faster than the respiration rate. The plant can therefore store most of the glucose. When there is not sunlight, only the respiration process occurs and the plant becomes a net consumer of oxygen. At low light conditions which for most plants is about two percent of full sunlight, photosynthesis and respiration are in balance at what is called the compensation point.

Photorespiration is another matter entirely. Based on the observation that the carbon dioxide fixation of the Calvin-Benson Cycle became more protracted as oxygen levels were increased, it was discovered that rubisco, the most common protein on earth and the catalyst for carbon fixation, had a small problem. Carbon dioxide has a characteristic special geometry with the two larger oxygen atoms at an oblique angle with the central carbon atom. Oxygen in the form of O2 has a very similar geometry, the two oxygen atoms adjacent without the carbon atom in the middle. Rubisco, like most if not all catalysts, utilizes geometric shape to align the catalyzed molecules so that they are in a proper position to bond. Since rubisco is at least somewhat ambivalent to the presence or absence of the carbon atom included in carbon dioxide, it will take an oxygen molecule instead of a carbon dioxide molecule and place it into the same 5 -carbon ribulose diphosphate. This creates an undesirable 2 -carbon compound called phosphoglycolate which is of no use to the plant. The process of photorespiration is the conversion of phosphoglycolate back into a usable compound, with an investment of ATP energy, in contrast to respiration which creates usable energy. In some plants and in some environmental conditions, photorespiration can subvert nearly fifty percent of the Calvin-Benson Cycle. It is thought that the photorespiration situation arose because the earth had very little oxygen when rubisco evolved (the Great Oxidation Event having not yet occurred) so that it had no need to differentiate between the two gases.

It is now fairly common knowledge that there are the 3-carbon plants that utilize the Calvin-Benson Cycle discussed above and that there are also 4-carbon plants. The so-called C3 plants include all trees, most cold-climate plants, and most agricultural plants, such as wheat and rice. The C4 plants include most tropical and temperate grasses, most arid plants, and some crops such as corn and sugar cane. The C4 cycle differs from the C3 Calvin-Benson Cycle in the way that carbon dioxide is handled. In C4 photosynthesis, CO2 is combined with a 3-carbon molecule called PEP (phosphoenolpyruvate) to create a 4-carbon compound (whence the name C4) which is converted and transferred to another part of the plant called the bundle sheath cells where the CO2 is stripped off and sent off to the rubisco of the Calvin-Benson Cycle. The C4 process results in elevated CO2 levels in area immediately adjacent to the rubisco which has the effect of significantly reducing photorespiration. The C4 version of photosynthesis arose primarily in grasses as they inhabit generally marginal environments where photorespiration is a more serious problem. The implications in a world where CO2 levels are rising are that C3 plants will increase their photosynthetic capacity which means that they will produce more usable glucose. Field experiments have demonstrated that C3 crops increase their photosynthesis by about 33 percent and that C3 trees increase their photosynthesis by about 60 percent with a doubling of CO2 levels in the atmosphere. C4 plants would not have this large of an increase due to their more efficient use of CO2.

The Carbon Cycle
The carbon cycle from the whole earth perspective consists of three interrelated repositories of carbon with a variety of mechanisms by which carbon is transferred from one to the other. These are the atmosphere, the terrestrial areas and the oceans. It is irrefutable that the atmospheric levels of carbon are of most concern, as it is the carbon in the form of CO2 that is the cause of global warming. Before discussing the magnitudes of carbon in the various repositories and fluxes or flows of carbon that operate between them, it is probably of value to address the units and relative magnitudes of carbon dioxide. To put things in perspective, a gallon of hydrocarbon gasoline weighs about 8 pounds which is for the most part carbon. When you oxidize or burn it for the energy that is stored in its bonds, you get carbon dioxide which means that each carbon is joined by two atoms of oxygen so that about 20 pounds of CO2 are added to the atmosphere for every gallon of gas used. If your automobile gets 20 miles per gallon, then you are generating about a pound of CO2 every mile. There are about 800 million cars and light trucks in the world which use about 250 billion gallons of fuel annually. This amounts to about 5 trillion pounds of CO2 per year just from passenger vehicles. Since a kilogram is about 2.2 pounds, this is about 2 trillion kilograms per year. The units used in the literature for carbon levels are either gigatonnes of carbon (GTC) or picograms of carbon (PgC) which are the same thing since a tonne is one thousand kilograms and 'giga' is the prefix for a billion and 'pico' is the prefix for a trillion (pico = mega x kilo). Therefore, all of the world's passenger vehicles discharge about 2 gigatonnes of CO2 annually which equates to about 1 gigatonne of carbon or 1 GTC per year.

According to the IPCC AR4 report, the atmosphere contains approximately 730 gigatonnes of carbon (GTC), the terrestrial areas contain 2,000 GTC and the oceans contain 38,000 GTC. The total amount of carbon added by fossil fuel burning and land use change is 5.3 GTC per year. Of this amount, 1.9 GTC per year is absorbed by the ocean and 0.2GTC per year is absorbed terrestrially leaving a net gain of only 3.2 GTC to the atmosphere. This does not seem all that dire, 3.2 GTC is less than a half a percent of the total atmospheric carbon of 730 GTC. This is one of the statistics employed to trivialize the CO2 problem by those who disagree with the science of climate. An understanding of the carbon cycle is necessary to explain why carbon dioxide, which comprises only 0.03 percent by volume of the atmosphere, has the potential to warm the earth to the point that human civilization would be in jeopardy.

Terrestrial Carbon

About one quarter of the total 2,000 GTC in terrestrial repositories is retained by plants (500 GTC) and the other three-quarters is retained in the soil (1,500 GTC). The plant carbon is sequestered in the biomass of the trees, the grasslands and the croplands that are the objects of the tropical rain forest, grazing and urbanization land use debates. When land is cleared of plants like tropical trees in favor of agricultural or ranching activities, the carbon capacity of the land is diminished; this is the core issue surrounding land use considerations. It is estimated that over the last two centuries, land-use changes have resulted in a total increase of about 200 GTC in the atmosphere. The soil carbon is comprised of the remains of the living plants and animals that have died and are or have been decomposing. There are three recognized soil groups distinguished according to the time frame of the decomposition, the process by which the carbon is returned to the atmosphere . The detritus (300 GTC) is near the surface and has a turnover time on the order of a decade. The modified soil carbon comprises the bulk of the total (1050 GTC) as the subsoil layer with a turnover rate that ranges from a decade to a century. Inert carbon is the third group, a relatively small contribution (150 GTC) that accounts for the soil carbon that is essentially fixed, like coal.

The atmospheric CO2 concentration is influenced by the flux of carbon into and out of the terrestrial repositories of plants and soil. The main component in the flow of carbon between the air and the land is the uptake of CO2 for the photosynthesis of glucose discussed above which the IPCC estimates at 120 GTC per year for all terrestrial biomass. However, one half of this (60 GTC/yr) is immediately returned to the atmosphere due to the respiration and the photorespiration necessary to counteract the rubisco oxygen recognition problem also discussed above. The 60 GTC per year that is absorbed by the plants when corrected for respiration is called Net Primary Production (NPP). This is the carbon that is incorporated into new plants and into the growth of old plants that range in size and complexity from algae to redwoods. However, nearly all of this carbon is returned to the atmosphere by the decay and decomposition of the plants by heterotrophic fungi and bacteria and by the ingestion and digestion of plants by heterotrophic animals (55 GTC/yr) and by forest and grassland fires (4 GTC/yr). It is estimated that the average carbon atom that leaves the atmosphere due to photosynthesis is returned to the atmosphere in about 10 years. After about 250 years when all but the Methuselah trees have lived, died and decomposed, essentially all of the carbon from terrestrial sequestration is back in the atmosphere. The net result of the uptake of carbon by the plants and soils (1.9 GTC/yr) and the loss of carbon storage due to land use changes (- 1.7 GTC/yr) is that terrestrial areas absorb a total of about 0.2 GTC per year.

Volcanism and Weathering

There are two other aspects of terrestrial carbon and carbon dioxide that must be taken into account in the overall carbon cycle: volcanism and the weathering of igneous and carbonate rocks. Volcanism is the release of molten magma from deep in the earth to the surface in the form of lava. The expulsion of lava is accompanied by water vapor, sulfur dioxide, carbon dioxide and solid particles. While a volcanic eruption is cataclysmic with global cooling attendant to the dispersal of atmospheric sulfates , its contribution to the overall CO2 level is marginal. The total carbon dioxide flux from all geothermal sources amount to less than 0.1 GTC per year. One of the more radical approaches to combating rising temperatures is called "engineered geology," or geoengineering in which measures are taken to either deflect the sun's rays directly or to absorb carbon dioxide with : are purportedly "artificial trees." The leading geoengineering plan is to inject sulfur dioxide into the atmosphere to replicate a volcanic event like the 1991 eruption Mount Pinatubo in the Philippines which expelled about 15 megatonnes of sulfur dioxide into the atmosphere and resulted in a 15 month long global temperature drop of half a degree Celsius.

Weathering is the process by which rocks are dissolved by rainwater, an essential mechanism of soil formation. The basic formula is the combination of water and carbon dioxide to form carbonic acid (H2CO3) according to:
H2O + CO2 à H2CO3

Like all acids, carbonic acid will chemically react with other compounds to form salts, which are then dissolved in rain water washing down mountains into rivers that make their way to the oceans. Igneous rocks are made up primarily of feldspar which contains aluminum (Al), silica (Si) and oxygen (O) in addition to one or two other elements of which potassium (K) is the most common. Potassium feldspar (2K(AlSi3O8) ) weathers according to:

2K(AlSi3O8) + H2O + H2CO3 à K2CO3 + Al2Si2O5(OH)4 + 4SiO2

The products formed are potassium carbonate (K2CO3), clay (Al2Si2O5(OH)4) and sand or silt (SiO2). The net effect of the weathering of igneous rocks is to remove a small amount of CO2 from the atmosphere. From the standpoint of the terrestrial carbon cycle, the net effect of volcanism which adds carbon dioxide and weathering which removes carbon dioxide is negligible since they are more or less in balance.

Ocean Carbon

Ocean carbon has a much more convoluted process than terrestrial carbon. The ocean contains about 38,000 gigatonnes of carbon (GTC), fourteen times more that the land and fifty times more than the atmosphere. It absorbs about 90 GTC per year from the atmosphere and returns about 88 GTC per year so that the ocean provides a net carbon sink of 1.9 GTC per year. The carbon dioxide taken up by the ocean, which is known as dissolved inorganic carbon (DIC) is soluble according to the following:

CO2 + H2O + CO3 (-2) ç=è 2HCO (-3) where (-2) and (-3) are the valence states of having 2 or 3 extra electrons

where CO3(-2) is a carbonate ion (with a charge of -2) and HCO(-3) is the bicarbonate ion (with a charge of - 3). The symbol ç=è means that the equation is in equilibrium which in this case is 1% non-ionic dissolved CO2, 8% carbonate ion and 91% bicarbonate ion. The problem from the carbon dioxide absorption perspective is that as CO2 goes up, more bicarbonate is produced (the equilibrium shifts to the right) which drives down the carbonate ion concentration which limits the amount of additional CO2 that can be absorbed. It would seem, however, that the vastness of the oceans would afford the ideal sink for carbon; an increase of only 2 percent would accommodate a doubling of CO2. The problem is that even though the atmosphere to ocean carbon dioxide transfer reaches equilibrium after about a year, this only affects the surface waters, a relatively thin and shallow layer. The main repository of pelagic carbon is in the deep waters. It is estimated that mixing of the surface layers with the intermediate layers in ocean uptake would take several hundred years and that the mixing with the deep waters would be on the order of 5,000 years. The oceans will simply not accommodate the increases in carbon dioxide at the rate at which fossil fuels are being consumed. In other words, 1.9 GTC per year absorption is all that we will get in the time scale of concern, which is this century.

A second factor that is of concern with the effects of increasing CO2 shifting the equilibrium to the right is that this causes an increase in the concentration of H+ which means that the oceans get more acidic; it is estimated that the PH of the oceans has dropped from about 8.2 to 8.1 over the last century. While this may seem like a trivial amount, recall that the PH scale is logarithmic (PH = -log[H+] with PH = 7 neutral and PH < 7 acidic); a 0.1 change in PH is equivalent to a 20 percent increase in hydrogen ion concentration. Marine organisms are very sensitive to changes in the acidity of the oceans, particularly those that form calcium carbonate as previously discussed. This effect is of particular concern in the corals that form the foundation of the reef habitats.

The ocean contains both plants and animals, most of which are the plankton, which are defined as small floating or weakly swimming organisms in a body of water; plant plankton are phytoplankton and animal plankton are zooplankton. It is estimated that the phytoplankton absorb 103 GTC per year, but, as was the case with the terrestrial plants, autotrophic respiration returns about 58 GTC back to the ocean pool of dissolved inorganic carbon (DIC). The remaining carbon of 45 GTC per year is the Net Primary Production (NPP) of phytoplankton (compared to an NPP of 60 GTC per year for terrestrial plants). The zooplankton, being heterotrophic, need to consume the phytoplankton for energy, and in doing so, they take in oxygen and give off carbon dioxide. This heterotrophic respiration restores about 34 GTC per year of carbon to the DIC ocean pool. The animal herbivores were not considered in the terrestrial carbon balance as they are much less of a factor than the ubiquitous zooplankton of the oceans. The phytoplankton that are not consumed and the zooplankton all eventually die and sink to the bottom of the ocean as dissolved organic carbon (DOC) which is estimated as 11 GTC per year. As the detritus comprised of dead plants and animals subsides, most is decomposed by heterotrophs in deeper waters that convert it DIC; a small amount estimated at about 0.1 GTC per year ends up in the sediments at the bottom of the ocean (the provenance of petroleum). The transport of carbon in the form of DIC is what is known as the biological pump; the continuous life and death cycle of marine organisms "pumping" carbon to deep water where it is retained for decades if not centuries. It is estimated that the level of CO2 in the atmosphere would be about 200 ppm higher (587 ppm instead of 387 ppm) than it is now without the effects of the biological pump.

The last element of the ocean carbon cycle to consider is the input from the terrestrial carbon cycle, as all rivers run to the sea. When bodies of water evaporate and return the condensation to land in the form of rain, erosion and weathering occur as discussed above. The carbon in the soil from plants and the carbon from the weathering of rocks (that may or may not have consolidated as soil) are carried by riparian waters to the estuaries of the ocean. It is estimated that the total carbon flux from all sources is 0.8 GTC per year of which three quarters returns to the atmosphere as CO2 and one quarter is buried in the sediment, mostly in neritic (near shore) deposits.

Marine animals such as mollusks form shells of calcium carbonate (CaCO3). This has the effect of reducing the ocean's carbonate ion concentration (CO3(-2) which drives the ocean carbon equation above to restore equilibrium, which is to the left. This results in an increase of CO2 which is counter to the removal of CO2 by these same marine organisms as dissolved organic carbon (DOC) The ratio of DOC to calcium carbonate (CaCO3) is known as the "rain ratio" and is used to characterize the biological driving force on atmospheric CO2. The value of the rain ratio is still very much an estimate even in the IPCC AR4 report, with values that range from 4 to 11. The total amount of CaCO3 produced by marine organisms is estimated as 0.7 GTC pre year with about half going to shallow coastal water sediments and the other half going to deep water sediments. Most if not all will eventually reappear in geological time frame as limestone. Limestone is a sedimentary rock that is formed by the buildup of calcareous shells over time, its presence in terrestrial environments the result of the uplifts of marine basins concomitant to tectonic orogenies. Limestone reacts with carbonic acid according to:

H2CO3 + CaCO3 à Ca+ + OH- + CO2

to release the carbon dioxide back to the atmosphere. The interaction of marine fauna in the carbon cycle in their use of carbon in their shells which depletes the carbon in the ocean while at the same time reducing the solubility of atmospheric carbon dioxide is testimony to the complexities of the ocean carbon cycle - further complicated on the geological time scale by the return of the original carbon stored in calcium carbonate to the atmosphere by the weathering of limestone.

Summary and Conclusions
Animals and fungi rely on plants to fix carbon from the atmosphere so that they can consume them to oxidize the carbon in the act of respiration to produce energy. Carbon is the basis for organisms and organic chemistry provides their architecture. The compound forming nature of elemental carbon is manifest in the carbon cycle that includes the carbon dioxide of the atmosphere, the carbon compounds of terrestrial and marine plants and animals, and the carbonate ions of the ocean waters. The carbon cycle is a balance that is established on a geologic scale. The carbon dioxide of the atmosphere is in equilibrium with land, exchanging about 120 GTC per year. The carbon dioxide of the atmosphere is in equilibrium with the oceans, exchanging about 90 GTC per year. The 5.4 GTC that is added almost entirely by the burning of fossil fuels is disturbing these equilibria.
Gilbert Plass was a professor at Johns Hopkins University working on infrared radiation with funding from the Office of Naval Research; his research led to an article in American Scientist, the journal of Sigma Xi, the Scientific Research Society in July, 1956 entitled "Carbon Dioxide and the Climate." The article addresses what was then known as the carbon dioxide theory as a means of explaining climate change - the other major contenders being variations in solar energy, volcanic dust, and changes in the elevation of continents. The thermodynamic argument for carbon dioxide is presented with logic and perspicacity: "… as the amount of carbon dioxide increases … the outgoing radiation is trapped more effectively near the Earth's surface and the temperature rises. The latest calculations show that if the carbon dioxide content of the atmosphere should double, the surface temperature would rise 3.6 degrees Celsius…" In the early 1950's there were no comprehensive data on the levels of carbon dioxide in the atmosphere and no ice core samples to correlate to historical norms. The article concludes with: "If at the end of this century the average temperature has continued to rise and in addition measurement also shows that the atmospheric carbon dioxide amount has also increased, then it will be firmly established that carbon dioxide is a determining factor in causing climate change." Atmospheric carbon dioxide monitoring began at the Mauna Loa observatory in March, 1958. Since that time, carbon dioxide has risen from 318 parts per million (ppm) to 387 ppm. The deepest ice core that was extracted at the Russian Vostok station in East Antarctica in January, 1998 revealed that the carbon dioxide had been below about 280 ppm for the last 420,000 years. It may therefore be logically concluded that anthropogenic carbon dioxide is the most likely cause of the increase in global temperatures.

The laws of ecology established by Barry Commoner in the last century are instructive in the understanding of the carbon cycle and the carbon dioxide problem. They are: (1) Everything is connected to everything else; (2) Everything must go somewhere; (3) Nature knows best; and (4) There is no free lunch. In terms of the carbon cycle: (1) The plants and the animals of the lands and oceans are all connected by carbon; (2) The carbon that is stored in plants and animals must eventually go somewhere else when they die; (3) Carbon dioxide will end up in the atmosphere because it is natural for it to do so; and (4) The burning of carbon sequestered over a millennial accumulation of plant-based coal and animal-based petroleum in the course of several hundred years is not and will not be a free lunch. The inexorable rise of carbon dioxide in the atmosphere is not going to stop and the inexorable rise in temperature will continue. The only answer is to either stop burning fossil fuel or figure out a way to collect the carbon dioxide that it generates.